Index

A

add_hcx_members_annotation() (in module cellmaps_utils.hcx_utils) add_hcx_network_annotations() (in module cellmaps_utils.hcx_utils) add_isroot_node_attribute() (in module cellmaps_utils.hcx_utils) add_subparser() (cellmaps_utils.apmstool.APMSDataLoader method) (cellmaps_utils.basecmdtool.BaseCommandLineTool static method) (cellmaps_utils.basecmdtool.HelloWorldCommand method) (cellmaps_utils.crisprtool.CRISPRDataLoader method) (cellmaps_utils.iftool.IFImageDataConverter method) (cellmaps_utils.tabletool.TableFromROCrates static method)

ANTIBODY_GENE_TABLE_FILE (in module cellmaps_utils.constants) APMS_TSV_FILE (in module cellmaps_utils.constants) APMSDataLoader (class in cellmaps_utils.apmstool) ArgParseFormatter (class in cellmaps_utils.constants)

B

BAIT_COL_NAME (cellmaps_utils.apmstool.APMSDataLoader attribute)

BaseCommandLineTool (class in cellmaps_utils.basecmdtool) BLUE (in module cellmaps_utils.constants)

C

canberra_similarity() (in module cellmaps_utils.music_utils) CELL_LINE_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) cellmaps_utils module cellmaps_utils.apmstool module cellmaps_utils.basecmdtool module cellmaps_utils.cellmaps_utilscmd module cellmaps_utils.constants module cellmaps_utils.crisprtool module cellmaps_utils.ddotconverter module cellmaps_utils.hcx_utils module cellmaps_utils.hidefconverter module cellmaps_utils.hierdiff module cellmaps_utils.iftool module cellmaps_utils.logutils module cellmaps_utils.music_utils module cellmaps_utils.ndexupload module

cellmaps_utils.provenance module cellmaps_utils.tabletool module CellMapsError (class in cellmaps_utils.exceptions) CellMapsProvenanceError (class in cellmaps_utils.exceptions) check_symmetric() (in module cellmaps_utils.music_utils) CO_EMBEDDING_FILE (in module cellmaps_utils.constants) COEMBEDDING_STEP_DIR (in module cellmaps_utils.constants) COLOR_INDEXS (in module cellmaps_utils.constants) COLOR_LABELS_MAP (in module cellmaps_utils.constants) COLORS (in module cellmaps_utils.constants) COLUMNS (cellmaps_utils.tabletool.TableFromROCrates attribute) COMMAND (cellmaps_utils.apmstool.APMSDataLoader attribute) (cellmaps_utils.basecmdtool.BaseCommandLineTool attribute) (cellmaps_utils.basecmdtool.HelloWorldCommand attribute) (cellmaps_utils.crisprtool.CRISPRDataLoader attribute) (cellmaps_utils.iftool.IFImageDataConverter attribute) (cellmaps_utils.tabletool.TableFromROCrates attribute) compare_hierarchies() (cellmaps_utils.hierdiff.HierarchyDiff method) compare_hierarchies_from_files() (cellmaps_utils.hierdiff.HierarchyDiff method) COMPUTATION_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) compute_hierarchy_robustness() (cellmaps_utils.hierdiff.HierarchyDiff method) convert_hierarchical_network_to_hcx() (in module cellmaps_utils.hcx_utils) cosine_similarity_scaled() (in module cellmaps_utils.music_utils) CRISPRDataLoader (class in cellmaps_utils.crisprtool) CX2_SUFFIX (in module cellmaps_utils.constants) CX_SUFFIX (in module cellmaps_utils.constants)

D

DATA_ROCRATE (cellmaps_utils.tabletool.TableFromROCrates attribute) DATASET_AUTHOR (in module cellmaps_utils.constants) DATASET_CELL_LINE (in module cellmaps_utils.constants) DATASET_COLLECTION_SET (in module cellmaps_utils.constants) DATASET_GENE_SET (in module cellmaps_utils.constants) DATASET_INFO_FILE (in module cellmaps_utils.constants) DATASET_NAME (in module cellmaps_utils.constants) DATASET_ORGANIZATION_NAME (in module cellmaps_utils.constants) DATASET_PROJECT_NAME (in module cellmaps_utils.constants) DATASET_RELEASE (in module cellmaps_utils.constants) DATASET_SLICE (in module cellmaps_utils.constants) DATASET_TISSUE (in module cellmaps_utils.constants)

DATASET_TREATMENT (in module cellmaps_utils.constants) DATE_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) DDOTToHierarchyConverter (class in cellmaps_utils.ddotconverter) DDOTToInteractomeConverter (class in cellmaps_utils.ddotconverter) DESCRIPTION_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) DOWNLOAD_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) DOWNLOAD_COL_SIZE (cellmaps_utils.tabletool.TableFromROCrates attribute) download_file() (in module cellmaps_utils.iftool) download_file_skip_existing() (in module cellmaps_utils.iftool) download_images() (cellmaps_utils.iftool.FakeImageDownloader method) (cellmaps_utils.iftool.ImageDownloader method) (cellmaps_utils.iftool.MultiProcessImageDownloader method)

E

ERROR_LOG_FILE (in module cellmaps_utils.constants)

euclidean_similarity() (in module cellmaps_utils.music_utils) example_dataset_provenance() (cellmaps_utils.provenance.ProvenanceUtil static method)

F

FakeImageDownloader (class in cellmaps_utils.iftool)

G

generate_ddot_format_file() (cellmaps_utils.ddotconverter.InteractomeToDDOTConverter method) generate_hidef_files() (cellmaps_utils.hidefconverter.HierarchyToHiDeFConverter method) generate_hierarchy_hcx_file() (cellmaps_utils.ddotconverter.DDOTToHierarchyConverter method) (cellmaps_utils.hidefconverter.HiDeFToHierarchyConverter method) generate_interactome_file() (cellmaps_utils.ddotconverter.DDOTToInteractomeConverter method) generate_ontology_ddot_file() (cellmaps_utils.ddotconverter.HierarchyToDDOTConverter method) GENERATED_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) GENESET_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) get_cytoscape_url() (cellmaps_utils.ndexupload.NDExHierarchyUploader method) get_default_date_format_str() (cellmaps_utils.provenance.ProvenanceUtil method) get_description() (cellmaps_utils.provenance.ROCrateProvenanceAttributes method) get_host_and_uuid_from_network_url() (in module cellmaps_utils.hcx_utils)

get_id_of_rocrate() (cellmaps_utils.provenance.ProvenanceUtil method) get_interactome() (in module cellmaps_utils.hcx_utils) get_keywords() (cellmaps_utils.provenance.ROCrateProvenanceAttributes method) get_login() (cellmaps_utils.provenance.ProvenanceUtil method) get_merged_rocrate_provenance_attrs() (cellmaps_utils.provenance.ProvenanceUtil method) get_name() (cellmaps_utils.provenance.ROCrateProvenanceAttributes method) get_name_project_org_of_rocrate() (cellmaps_utils.provenance.ProvenanceUtil method) get_organization_name() (cellmaps_utils.provenance.ROCrateProvenanceAttributes method) get_project_name() (cellmaps_utils.provenance.ROCrateProvenanceAttributes method) get_rocrate_as_dict() (cellmaps_utils.provenance.ProvenanceUtil method) get_rocrate_provenance_attributes() (cellmaps_utils.provenance.ProvenanceUtil method) get_root_nodes() (in module cellmaps_utils.hcx_utils) GREEN (in module cellmaps_utils.constants)

H

HCX_SUFFIX (in module cellmaps_utils.constants) HelloWorldCommand (class in cellmaps_utils.basecmdtool) HIDEF_OUT_PREFIX (cellmaps_utils.hidefconverter.HierarchyToHiDeFConverter attribute) HiDeFToHierarchyConverter (class in cellmaps_utils.hidefconverter) HIERARCHY_NETWORK_PREFIX (in module cellmaps_utils.constants) HIERARCHY_NODES_FILE (in module cellmaps_utils.constants)

HIERARCHY_PARENT_NETWORK_PREFIX (in module cellmaps_utils.constants) HIERARCHY_STEP_DIR (in module cellmaps_utils.constants) HierarchyDiff (class in cellmaps_utils.hierdiff) HIERARCHYEVAL_STEP_DIR (in module cellmaps_utils.constants) HierarchyToDDOTConverter (class in cellmaps_utils.ddotconverter) HierarchyToHiDeFConverter (class in cellmaps_utils.hidefconverter)

I

ID_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) IFImageDataConverter (class in cellmaps_utils.iftool) IMAGE_DOWNLOAD_STEP_DIR (in module cellmaps_utils.constants) IMAGE_EMBEDDING_FILE (in module cellmaps_utils.constants) IMAGE_EMBEDDING_STEP_DIR (in module cellmaps_utils.constants) IMAGE_GENE_NODE_AMBIGUOUS_COL (in module cellmaps_utils.constants) IMAGE_GENE_NODE_ANTIBODY_COL (in module cellmaps_utils.constants) IMAGE_GENE_NODE_ATTR_FILE (in module cellmaps_utils.constants) IMAGE_GENE_NODE_COLS (in module cellmaps_utils.constants)

IMAGE_GENE_NODE_ERRORS_FILE (in module cellmaps_utils.constants) IMAGE_GENE_NODE_FILENAME_COL (in module cellmaps_utils.constants) IMAGE_GENE_NODE_IMAGEURL_COL (in module cellmaps_utils.constants) IMAGE_GENE_NODE_NAME_COL (in module cellmaps_utils.constants) IMAGE_GENE_NODE_REPRESENTS_COL (in module cellmaps_utils.constants) IMAGE_LABELS_PROBABILITY_FILE (in module cellmaps_utils.constants) ImageDownloader (class in cellmaps_utils.iftool) InteractomeToDDOTConverter (class in cellmaps_utils.ddotconverter) INTERMEDIATE_ROCRATE (cellmaps_utils.tabletool.TableFromROCrates attribute)

J

jaccard() (in module cellmaps_utils.music_utils)

K

kendall_scaled() (in module cellmaps_utils.music_utils)

KEYWORDS_COL (cellmaps_utils.tabletool.TableFromROCrates attribute)

L

load_obj() (in module cellmaps_utils.music_utils)

LOG_FORMAT (in module cellmaps_utils.constants)

M

main() (in module cellmaps_utils.cellmaps_utilscmd) manhattan_similarity() (in module cellmaps_utils.music_utils) MODEL_ROCRATE (cellmaps_utils.tabletool.TableFromROCrates attribute) module cellmaps_utils cellmaps_utils.apmstool cellmaps_utils.basecmdtool cellmaps_utils.cellmaps_utilscmd cellmaps_utils.constants cellmaps_utils.crisprtool cellmaps_utils.ddotconverter cellmaps_utils.hcx_utils cellmaps_utils.hidefconverter cellmaps_utils.hierdiff cellmaps_utils.iftool cellmaps_utils.logutils cellmaps_utils.music_utils cellmaps_utils.ndexupload cellmaps_utils.provenance cellmaps_utils.tabletool

MultiProcessImageDownloader (class in cellmaps_utils.iftool)

N

NDExHierarchyUploader (class in cellmaps_utils.ndexupload)

num_comb() (in module cellmaps_utils.music_utils)

O

OTHER_ROCRATE (cellmaps_utils.tabletool.TableFromROCrates attribute)

OUTPUT_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) OUTPUT_LOG_FILE (in module cellmaps_utils.constants)

P

pearson_scaled() (in module cellmaps_utils.music_utils) PERTURBATION_FILE (in module cellmaps_utils.constants) PPI_DOWNLOAD_STEP_DIR (in module cellmaps_utils.constants) PPI_EDGELIST_COLS (in module cellmaps_utils.constants) PPI_EDGELIST_FILE (in module cellmaps_utils.constants) PPI_EDGELIST_GENEA_COL (in module cellmaps_utils.constants) PPI_EDGELIST_GENEB_COL (in module cellmaps_utils.constants)

PPI_EMBEDDING_FILE (in module cellmaps_utils.constants) PPI_EMBEDDING_STEP_DIR (in module cellmaps_utils.constants) PPI_GENE_NODE_ATTR_FILE (in module cellmaps_utils.constants) PPI_GENE_NODE_COLS (in module cellmaps_utils.constants) PPI_GENE_NODE_ERRORS_FILE (in module cellmaps_utils.constants) PROVENANCE_ERRORS_FILE (in module cellmaps_utils.constants) ProvenanceUtil (class in cellmaps_utils.provenance)

R

RED (in module cellmaps_utils.constants) register_computation() (cellmaps_utils.provenance.ProvenanceUtil method) register_dataset() (cellmaps_utils.provenance.ProvenanceUtil method) register_rocrate() (cellmaps_utils.provenance.ProvenanceUtil method) register_software() (cellmaps_utils.provenance.ProvenanceUtil method) RESPONSIBLE_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) RO_CRATE_METADATA_FILE (in module cellmaps_utils.constants)

ROCrateProvenanceAttributes (class in cellmaps_utils.provenance) run() (cellmaps_utils.apmstool.APMSDataLoader method) (cellmaps_utils.basecmdtool.BaseCommandLineTool method) (cellmaps_utils.basecmdtool.HelloWorldCommand method) (cellmaps_utils.crisprtool.CRISPRDataLoader method) (cellmaps_utils.iftool.IFImageDataConverter method) (cellmaps_utils.tabletool.TableFromROCrates method)

S

save_dataset_info_to_json() (cellmaps_utils.basecmdtool.BaseCommandLineTool method) save_hierarchy_and_parent_network() (cellmaps_utils.ndexupload.NDExHierarchyUploader method) save_obj() (in module cellmaps_utils.music_utils)

scaled_P_to_nm() (in module cellmaps_utils.music_utils) setup_cmd_logging() (in module cellmaps_utils.logutils) setup_filelogger() (in module cellmaps_utils.logutils) spearman_scaled() (in module cellmaps_utils.music_utils)

T

TableFromROCrates (class in cellmaps_utils.tabletool) TASK_FILE_PREFIX (in module cellmaps_utils.constants) TASK_FINISH_FILE_SUFFIX (in module cellmaps_utils.constants)

TASK_START_FILE_SUFFIX (in module cellmaps_utils.constants) TISSUE_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) TREATMENT_COL (cellmaps_utils.tabletool.TableFromROCrates attribute) TYPE_COL (cellmaps_utils.tabletool.TableFromROCrates attribute)

U

upload_hierarchy_and_parent_network_from_files() (cellmaps_utils.ndexupload.NDExHierarchyUploader method)

upper_tri_values() (in module cellmaps_utils.music_utils)

V

VERSION_COL (cellmaps_utils.tabletool.TableFromROCrates attribute)

W

WEIGHTED_PPI_EDGELIST_WEIGHT_COL (in module cellmaps_utils.constants)

write_task_finish_json() (in module cellmaps_utils.logutils) write_task_start_json() (in module cellmaps_utils.logutils)

Y

YELLOW (in module cellmaps_utils.constants)

Z

znorm() (in module cellmaps_utils.music_utils)